R/alignment.R
In tangshao2016/neoantigenR: neoantigen prediction from NGS sequencing data
Defines functions
neoantigenR.get.peptides
Documented in
neoantigenR.get.peptides
##-----------------------------------
## main function module 2 : alignment
##-----------------------------------
## compute neoantigens using the novel algorithm after the preparation steps
#' compute neoantigens using the novel algorithm after the preparation steps
#' @return no values will be returned
neoantigenR.get.peptides<-function(){
alignment.indel.detailed.info.table = data.frame()
for(chosen.gene in target.gene.list){
input.file.name=file.path(dataDir, paste(chosen.gene, ".pacbio.dnaseq.protein.sequence.txt", sep=""))
if(!is.na(file.size(input.file.name)) & file.size(input.file.name)>0){
database.name=chosen.gene
matched.database.index=which(uniprot.protein.names.new==chosen.gene & uniprot.protein.swissprot.index==1) ## only swiss-prot ?
if(length(matched.database.index)>0){
mySequences.all <- readAAStringSet(input.file.name) #Biostrings::readAAStringSet
num.unique.isoforms=round(length(mySequences.all)/6)
#forward.strand.isoform.idx=c(seq(from=1,to=num.unique.isoforms*6,by=6), seq(from=2,to=num.unique.isoforms*6,by=6),seq(from=3,to=num.unique.isoforms*6,by=6)) #1:(num.unique.isoforms*6)
forward.strand.isoform.idx=1:(num.unique.isoforms*6) # 11/7/2017
for(n.isof in forward.strand.isoform.idx){
ref.sequence.name=names(attributes(mySequences.all[n.isof])$ranges)
if(length(grep("_R_", ref.sequence.name))>0 | length(grep("_F_", ref.sequence.name))>0){
ref.sequence.name=substr(ref.sequence.name, 1, nchar(ref.sequence.name)-4)
}
database.seq.isoforms=unlist(lapply(matched.database.index, function(idx){uniprot.human.database[[idx]][1]}))
for(ds.idx in 1:length(database.seq.isoforms)){
database.isoform.name=attributes(uniprot.human.database[[matched.database.index[ds.idx]]])$Annot
database.isoform.uniprotID=strsplit(database.isoform.name, "|",fixed=TRUE)[[1]][2]
reference.sequence=toString(mySequences.all[n.isof])
database.sequence=database.seq.isoforms[ds.idx]
mySequences.new=union(reference.sequence, database.sequence) # database.seq.isoforms)
myFirstAlignment=msa::msa(mySequences.new, order="input", type="protein")
reference.sequence=gsub("-","z", reference.sequence) # z for stop
pacbio.protein.sequences=reference.sequence
alignment.full.details.strings=msa::msaConvert(myFirstAlignment, type="bios2mds::align")
alignment.full.details.matrix=matrix("", length(alignment.full.details.strings), length(alignment.full.details.strings[[1]]))
for(i in 1:length(alignment.full.details.strings)){
alignment.full.details.matrix[i,]=alignment.full.details.strings[[i]]
}
alignment.matrix=alignment.full.details.matrix
identity.not.equal.vector=rep(0, ncol(alignment.matrix))
identity.equal.matrix=matrix(0, nrow(alignment.matrix)-1, ncol(alignment.matrix))
for(i in 1:ncol(alignment.matrix)){
if(length(unique(alignment.matrix[1:nrow(alignment.matrix),i]))==1){
identity.not.equal.vector[i]=0
identity.equal.matrix[1:(nrow(alignment.matrix)-1),i]=1
}else if(alignment.matrix[1,i]!="-" & length(unique(alignment.matrix[2:nrow(alignment.matrix),i]))==1 &
unique(alignment.matrix[2:nrow(alignment.matrix),i])[1]=="-"){
identity.not.equal.vector[i]=1
}else if(alignment.matrix[1,i]=="-" & length(unique(alignment.matrix[2:nrow(alignment.matrix),i]))==1 &
unique(alignment.matrix[2:nrow(alignment.matrix),i])[1]!="-"){
identity.not.equal.vector[i]=-1
}else{
identity.not.equal.vector[i]=2
identity.equal.matrix[which(alignment.matrix[2:nrow(alignment.matrix),i]==alignment.matrix[1,i]),i]=1
}
}
if(length(which(identity.not.equal.vector==0))>minimum.sequence.similarity*(min(c(nchar(reference.sequence), nchar(database.sequence))))){
k=1
mismatch.indel.regions=list()
prev.end=0;curr.start=0
cnt=0
new.common.seq=TRUE
for(j in 1:length(identity.not.equal.vector)){
if(identity.not.equal.vector[j]==0){
if(new.common.seq==TRUE){ # leading 0
cnt=1
curr.start=j-1 # a new start
new.common.seq=FALSE
}else{
cnt=cnt+1
}
if(prev.end>0 & cnt>=minimum.flanking.region.size &
(curr.start-prev.end)>=min.mismatch.size & (curr.start-prev.end)<=max.mismatch.size){ # delete the following condition 5/24/2017
## & (length(which(identity.not.equal.vector==0))/length(identity.not.equal.vector))>=minimum.sequence.similarity){ # minimum.alignment.match.ratio){
this.mismatch.indel.region=c(prev.end, curr.start)
left.flanking.seq=paste(alignment.matrix[1, (prev.end-minimum.flanking.region.size):(prev.end-1)], collapse="")
right.flanking.seq=paste(alignment.matrix[1, (curr.start+1):(curr.start+minimum.flanking.region.size)], collapse="")
mismatch.indel.region.seq=paste(alignment.matrix[1, prev.end:curr.start], collapse="")
mismatch.indel.region.seq=gsub("\\-", "", mismatch.indel.region.seq) # could be all "---" if deletions
if(regexpr(mismatch.indel.region.seq, reference.sequence)[1]!=(-1) &
regexpr("-", left.flanking.seq)[1]<0 & regexpr("-", right.flanking.seq)[1]<0){
mismatch.indel.regions[[k]]=this.mismatch.indel.region;k=k+1
}
prev.end=0 # reset the prev.end, but keep the counter
}
}
if(identity.not.equal.vector[j]!=0 & cnt>0){
new.common.seq=TRUE
if(cnt>=minimum.flanking.region.size){ # a valid left flanking sequence, so a begining of mismatch/indel
prev.end=j
cnt=0 # reset counter
}
}
}
if(length(mismatch.indel.regions)>0){
for(pr in 1:length(mismatch.indel.regions)){
prev.end =mismatch.indel.regions[[pr]][1]
curr.start=mismatch.indel.regions[[pr]][2]
indel.region.vals=identity.not.equal.vector[prev.end:curr.start]
type.indel.region=
if(length(unique(indel.region.vals))==1){
if(unique(indel.region.vals)==(-1)){
"deletion"
}else if(unique(indel.region.vals)==1){
"insertion"
}else{
"mismatch"
}
}else{
"mismatch"
}
indel.seq=
if(type.indel.region=="deletion"){
paste(alignment.matrix[1, c((prev.end-minimum.flanking.region.size):(prev.end-1),(curr.start+1):(curr.start+minimum.flanking.region.size))], collapse="")
}else{
paste(alignment.matrix[1, prev.end:curr.start], collapse="")
}
indel.seq.larger=indel.seq # extend both size for 10 AA for neoantigen prediction
if(type.indel.region!="deletion"){
left.end=prev.end-10
right.end=curr.start+10
if(left.end<1){left.end=1}
if(right.end>dim(alignment.matrix)[2]){right.end=dim(alignment.matrix)[2]}
indel.seq.larger=paste(alignment.matrix[1, left.end:right.end], collapse="")
}
indel.region.seq.overlap.ratio=0
reference.indel.region.seq=""
if(type.indel.region=="mismatch"){
reference.indel.region.seq=paste(alignment.matrix[2, prev.end:curr.start], collapse="")
reference.indel.region.seq=gsub("\\-", "", reference.indel.region.seq)
indel.region.seq.overlap.ratio=(1-round(length(which(indel.region.vals==2))/length(indel.region.vals),2))
}
if(type.indel.region=="deletion"){
reference.indel.region.seq=paste(alignment.matrix[2, prev.end:curr.start], collapse="")
}
indel.seq.no.hypen=gsub("\\-", "", indel.seq)
if(nchar(indel.seq.no.hypen)/nchar(indel.seq)<0.200000){
indel.seq=paste(alignment.matrix[2, prev.end:curr.start], collapse="") # must be a deletion, any database isoform is good
}
indel.seq=gsub("\\-", "", indel.seq)
match.all.database.isoforms.index=
if(nchar(indel.seq)<1460){
attributes(regexpr(indel.seq, database.seq.isoforms))$match.length
}else{
1
}
if(validate.in.database.boolean==FALSE | (validate.in.database.boolean==TRUE & max(match.all.database.isoforms.index)<0)){
chose.pacbio.transcript.id=as.vector(sample.pacbio.gencode.id.mapping[which(sample.pacbio.gencode.id.mapping[,2]==chosen.gene), 1])
pacbio.transcript.index=ceiling(n.isof/6) # if(n.isof%%6==0){n.isof/6}else{round(n.isof/6)+1}
chose.pacbio.transcript.id=strsplit(chose.pacbio.transcript.id[pacbio.transcript.index], ";")[[1]][1] # need global variable from function above Line-1246
output.file.name=file.path(dataDir, paste(chosen.gene, ".", chose.pacbio.transcript.id, ".F", n.isof, ".Ref", ds.idx, ".pacbio.dnaseq.protein.msa.txt", sep=""))
sink(output.file.name)
print(myFirstAlignment, show="complete")
cat("\n")
sink()
cat(prev.end, " ", curr.start, " ", indel.seq, "\n")
if(type.indel.region=="deletion"){
curr.start=prev.end-1
prev.end=prev.end-minimum.flanking.region.size
}
if(type.indel.region=="mismatch"){
curr.start=prev.end+nchar(indel.seq)-1
}
indel.pacbio.info=as.vector(unlist(find.indels.location.by.location(chosen.gene, chose.pacbio.transcript.id, indel.seq, pacbio.protein.sequences,
gene.df.pacbio, reference.gff.info.chosen, pacbio.isof.ids, compute.query.exon.details, compute.database.exon.details)))
average.coverage=0
# prev.end is the location in the alignment matrix, not from its original sequence
indel.seq.pos=regexpr(indel.seq, reference.sequence)[1]
prev.end.new=indel.seq.pos
curr.start.new=prev.end.new + (curr.start-prev.end)
indel.seq.detailed.info=c(chosen.gene, ref.sequence.name, database.isoform.name, prev.end.new, curr.start.new, prev.end.new*3-2, curr.start.new*3, indel.seq, average.coverage, n.isof, reference.indel.region.seq, indel.region.seq.overlap.ratio, type.indel.region, database.isoform.uniprotID, indel.seq.larger, indel.pacbio.info)
if(length(indel.seq.detailed.info)<36){
indel.seq.detailed.info=c(indel.seq.detailed.info, rep("", 36-length(indel.seq.detailed.info)))
}
indel.seq.detailed.info=t(data.frame(indel.seq.detailed.info))
colnames(indel.seq.detailed.info)=c("Gene","PacBioSequenceID","UniprotProteinID","ProteinStart","ProteinEnd","DNAStart","DNAEnd","IndelSequence","Coverage","Isof.Index", "reference.indel.region.seq", "indel.region.seq.overlap.ratio", "type", "uniprotID", "IndelSequenceAnchorSeq", "IndepPositioninGenome","Chrom","PacBio","region","PacBioStart","PacbioEnd","dot","strand","dot2","PacbioTranscriptID","ReferenceChrom","Reference_exon_start","Reference_exon_end", "dot3", "geneName", "strand2", "exontype","geneID","exonID","transcriptID","unkonwn")
if(nrow(alignment.indel.detailed.info.table)==0){
alignment.indel.detailed.info.table=indel.seq.detailed.info
}else{
alignment.indel.detailed.info.table=rbind(alignment.indel.detailed.info.table, indel.seq.detailed.info) ## Error in match.names(clabs, names(xi)) : names do not match previous names
}
}
}
}
}
}
}
}
}
}
if(nrow(alignment.indel.detailed.info.table)>0){
colnames(alignment.indel.detailed.info.table)=c("Gene","PacBioSequenceID","UniprotProteinID","ProteinStart","ProteinEnd","DNAStart","DNAEnd","IndelSequence","Coverage","Isof.Index", "reference.indel.region.seq", "indel.region.seq.overlap.ratio", "type", "uniprotID", "IndelSequenceAnchorSeq", "IndepPositioninGenome","Chrom","PacBio","region","PacBioStart","PacbioEnd","dot","strand","dot2","PacbioTranscriptID","ReferenceChrom","Reference_exon_start","Reference_exon_end", "dot3", "geneName", "strand2", "exontype","geneID","exonID","transcriptID","unkonwn")
}
#print(alignment.indel.detailed.info.table)
alignment.indel.detailed.info.table <<- alignment.indel.detailed.info.table
#print(alignment.indel.detailed.info.table)
}
tangshao2016/neoantigenR documentation built on May 21, 2019, 3:04 a.m.
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Defines functions neoantigenR.get.peptides
Documented in neoantigenR.get.peptides
##-----------------------------------
## main function module 2 : alignment
##-----------------------------------
## compute neoantigens using the novel algorithm after the preparation steps
#' compute neoantigens using the novel algorithm after the preparation steps
#' @return no values will be returned
neoantigenR.get.peptides<-function(){
alignment.indel.detailed.info.table = data.frame()
for(chosen.gene in target.gene.list){
input.file.name=file.path(dataDir, paste(chosen.gene, ".pacbio.dnaseq.protein.sequence.txt", sep=""))
if(!is.na(file.size(input.file.name)) & file.size(input.file.name)>0){
database.name=chosen.gene
matched.database.index=which(uniprot.protein.names.new==chosen.gene & uniprot.protein.swissprot.index==1) ## only swiss-prot ?
if(length(matched.database.index)>0){
mySequences.all <- readAAStringSet(input.file.name) #Biostrings::readAAStringSet
num.unique.isoforms=round(length(mySequences.all)/6)
#forward.strand.isoform.idx=c(seq(from=1,to=num.unique.isoforms*6,by=6), seq(from=2,to=num.unique.isoforms*6,by=6),seq(from=3,to=num.unique.isoforms*6,by=6)) #1:(num.unique.isoforms*6)
forward.strand.isoform.idx=1:(num.unique.isoforms*6) # 11/7/2017
for(n.isof in forward.strand.isoform.idx){
ref.sequence.name=names(attributes(mySequences.all[n.isof])$ranges)
if(length(grep("_R_", ref.sequence.name))>0 | length(grep("_F_", ref.sequence.name))>0){
ref.sequence.name=substr(ref.sequence.name, 1, nchar(ref.sequence.name)-4)
}
database.seq.isoforms=unlist(lapply(matched.database.index, function(idx){uniprot.human.database[[idx]][1]}))
for(ds.idx in 1:length(database.seq.isoforms)){
database.isoform.name=attributes(uniprot.human.database[[matched.database.index[ds.idx]]])$Annot
database.isoform.uniprotID=strsplit(database.isoform.name, "|",fixed=TRUE)[[1]][2]
reference.sequence=toString(mySequences.all[n.isof])
database.sequence=database.seq.isoforms[ds.idx]
mySequences.new=union(reference.sequence, database.sequence) # database.seq.isoforms)
myFirstAlignment=msa::msa(mySequences.new, order="input", type="protein")
reference.sequence=gsub("-","z", reference.sequence) # z for stop
pacbio.protein.sequences=reference.sequence
alignment.full.details.strings=msa::msaConvert(myFirstAlignment, type="bios2mds::align")
alignment.full.details.matrix=matrix("", length(alignment.full.details.strings), length(alignment.full.details.strings[[1]]))
for(i in 1:length(alignment.full.details.strings)){
alignment.full.details.matrix[i,]=alignment.full.details.strings[[i]]
}
alignment.matrix=alignment.full.details.matrix
identity.not.equal.vector=rep(0, ncol(alignment.matrix))
identity.equal.matrix=matrix(0, nrow(alignment.matrix)-1, ncol(alignment.matrix))
for(i in 1:ncol(alignment.matrix)){
if(length(unique(alignment.matrix[1:nrow(alignment.matrix),i]))==1){
identity.not.equal.vector[i]=0
identity.equal.matrix[1:(nrow(alignment.matrix)-1),i]=1
}else if(alignment.matrix[1,i]!="-" & length(unique(alignment.matrix[2:nrow(alignment.matrix),i]))==1 &
unique(alignment.matrix[2:nrow(alignment.matrix),i])[1]=="-"){
identity.not.equal.vector[i]=1
}else if(alignment.matrix[1,i]=="-" & length(unique(alignment.matrix[2:nrow(alignment.matrix),i]))==1 &
unique(alignment.matrix[2:nrow(alignment.matrix),i])[1]!="-"){
identity.not.equal.vector[i]=-1
}else{
identity.not.equal.vector[i]=2
identity.equal.matrix[which(alignment.matrix[2:nrow(alignment.matrix),i]==alignment.matrix[1,i]),i]=1
}
}
if(length(which(identity.not.equal.vector==0))>minimum.sequence.similarity*(min(c(nchar(reference.sequence), nchar(database.sequence))))){
k=1
mismatch.indel.regions=list()
prev.end=0;curr.start=0
cnt=0
new.common.seq=TRUE
for(j in 1:length(identity.not.equal.vector)){
if(identity.not.equal.vector[j]==0){
if(new.common.seq==TRUE){ # leading 0
cnt=1
curr.start=j-1 # a new start
new.common.seq=FALSE
}else{
cnt=cnt+1
}
if(prev.end>0 & cnt>=minimum.flanking.region.size &
(curr.start-prev.end)>=min.mismatch.size & (curr.start-prev.end)<=max.mismatch.size){ # delete the following condition 5/24/2017
## & (length(which(identity.not.equal.vector==0))/length(identity.not.equal.vector))>=minimum.sequence.similarity){ # minimum.alignment.match.ratio){
this.mismatch.indel.region=c(prev.end, curr.start)
left.flanking.seq=paste(alignment.matrix[1, (prev.end-minimum.flanking.region.size):(prev.end-1)], collapse="")
right.flanking.seq=paste(alignment.matrix[1, (curr.start+1):(curr.start+minimum.flanking.region.size)], collapse="")
mismatch.indel.region.seq=paste(alignment.matrix[1, prev.end:curr.start], collapse="")
mismatch.indel.region.seq=gsub("\\-", "", mismatch.indel.region.seq) # could be all "---" if deletions
if(regexpr(mismatch.indel.region.seq, reference.sequence)[1]!=(-1) &
regexpr("-", left.flanking.seq)[1]<0 & regexpr("-", right.flanking.seq)[1]<0){
mismatch.indel.regions[[k]]=this.mismatch.indel.region;k=k+1
}
prev.end=0 # reset the prev.end, but keep the counter
}
}
if(identity.not.equal.vector[j]!=0 & cnt>0){
new.common.seq=TRUE
if(cnt>=minimum.flanking.region.size){ # a valid left flanking sequence, so a begining of mismatch/indel
prev.end=j
cnt=0 # reset counter
}
}
}
if(length(mismatch.indel.regions)>0){
for(pr in 1:length(mismatch.indel.regions)){
prev.end =mismatch.indel.regions[[pr]][1]
curr.start=mismatch.indel.regions[[pr]][2]
indel.region.vals=identity.not.equal.vector[prev.end:curr.start]
type.indel.region=
if(length(unique(indel.region.vals))==1){
if(unique(indel.region.vals)==(-1)){
"deletion"
}else if(unique(indel.region.vals)==1){
"insertion"
}else{
"mismatch"
}
}else{
"mismatch"
}
indel.seq=
if(type.indel.region=="deletion"){
paste(alignment.matrix[1, c((prev.end-minimum.flanking.region.size):(prev.end-1),(curr.start+1):(curr.start+minimum.flanking.region.size))], collapse="")
}else{
paste(alignment.matrix[1, prev.end:curr.start], collapse="")
}
indel.seq.larger=indel.seq # extend both size for 10 AA for neoantigen prediction
if(type.indel.region!="deletion"){
left.end=prev.end-10
right.end=curr.start+10
if(left.end<1){left.end=1}
if(right.end>dim(alignment.matrix)[2]){right.end=dim(alignment.matrix)[2]}
indel.seq.larger=paste(alignment.matrix[1, left.end:right.end], collapse="")
}
indel.region.seq.overlap.ratio=0
reference.indel.region.seq=""
if(type.indel.region=="mismatch"){
reference.indel.region.seq=paste(alignment.matrix[2, prev.end:curr.start], collapse="")
reference.indel.region.seq=gsub("\\-", "", reference.indel.region.seq)
indel.region.seq.overlap.ratio=(1-round(length(which(indel.region.vals==2))/length(indel.region.vals),2))
}
if(type.indel.region=="deletion"){
reference.indel.region.seq=paste(alignment.matrix[2, prev.end:curr.start], collapse="")
}
indel.seq.no.hypen=gsub("\\-", "", indel.seq)
if(nchar(indel.seq.no.hypen)/nchar(indel.seq)<0.200000){
indel.seq=paste(alignment.matrix[2, prev.end:curr.start], collapse="") # must be a deletion, any database isoform is good
}
indel.seq=gsub("\\-", "", indel.seq)
match.all.database.isoforms.index=
if(nchar(indel.seq)<1460){
attributes(regexpr(indel.seq, database.seq.isoforms))$match.length
}else{
1
}
if(validate.in.database.boolean==FALSE | (validate.in.database.boolean==TRUE & max(match.all.database.isoforms.index)<0)){
chose.pacbio.transcript.id=as.vector(sample.pacbio.gencode.id.mapping[which(sample.pacbio.gencode.id.mapping[,2]==chosen.gene), 1])
pacbio.transcript.index=ceiling(n.isof/6) # if(n.isof%%6==0){n.isof/6}else{round(n.isof/6)+1}
chose.pacbio.transcript.id=strsplit(chose.pacbio.transcript.id[pacbio.transcript.index], ";")[[1]][1] # need global variable from function above Line-1246
output.file.name=file.path(dataDir, paste(chosen.gene, ".", chose.pacbio.transcript.id, ".F", n.isof, ".Ref", ds.idx, ".pacbio.dnaseq.protein.msa.txt", sep=""))
sink(output.file.name)
print(myFirstAlignment, show="complete")
cat("\n")
sink()
cat(prev.end, " ", curr.start, " ", indel.seq, "\n")
if(type.indel.region=="deletion"){
curr.start=prev.end-1
prev.end=prev.end-minimum.flanking.region.size
}
if(type.indel.region=="mismatch"){
curr.start=prev.end+nchar(indel.seq)-1
}
indel.pacbio.info=as.vector(unlist(find.indels.location.by.location(chosen.gene, chose.pacbio.transcript.id, indel.seq, pacbio.protein.sequences,
gene.df.pacbio, reference.gff.info.chosen, pacbio.isof.ids, compute.query.exon.details, compute.database.exon.details)))
average.coverage=0
# prev.end is the location in the alignment matrix, not from its original sequence
indel.seq.pos=regexpr(indel.seq, reference.sequence)[1]
prev.end.new=indel.seq.pos
curr.start.new=prev.end.new + (curr.start-prev.end)
indel.seq.detailed.info=c(chosen.gene, ref.sequence.name, database.isoform.name, prev.end.new, curr.start.new, prev.end.new*3-2, curr.start.new*3, indel.seq, average.coverage, n.isof, reference.indel.region.seq, indel.region.seq.overlap.ratio, type.indel.region, database.isoform.uniprotID, indel.seq.larger, indel.pacbio.info)
if(length(indel.seq.detailed.info)<36){
indel.seq.detailed.info=c(indel.seq.detailed.info, rep("", 36-length(indel.seq.detailed.info)))
}
indel.seq.detailed.info=t(data.frame(indel.seq.detailed.info))
colnames(indel.seq.detailed.info)=c("Gene","PacBioSequenceID","UniprotProteinID","ProteinStart","ProteinEnd","DNAStart","DNAEnd","IndelSequence","Coverage","Isof.Index", "reference.indel.region.seq", "indel.region.seq.overlap.ratio", "type", "uniprotID", "IndelSequenceAnchorSeq", "IndepPositioninGenome","Chrom","PacBio","region","PacBioStart","PacbioEnd","dot","strand","dot2","PacbioTranscriptID","ReferenceChrom","Reference_exon_start","Reference_exon_end", "dot3", "geneName", "strand2", "exontype","geneID","exonID","transcriptID","unkonwn")
if(nrow(alignment.indel.detailed.info.table)==0){
alignment.indel.detailed.info.table=indel.seq.detailed.info
}else{
alignment.indel.detailed.info.table=rbind(alignment.indel.detailed.info.table, indel.seq.detailed.info) ## Error in match.names(clabs, names(xi)) : names do not match previous names
}
}
}
}
}
}
}
}
}
}
if(nrow(alignment.indel.detailed.info.table)>0){
colnames(alignment.indel.detailed.info.table)=c("Gene","PacBioSequenceID","UniprotProteinID","ProteinStart","ProteinEnd","DNAStart","DNAEnd","IndelSequence","Coverage","Isof.Index", "reference.indel.region.seq", "indel.region.seq.overlap.ratio", "type", "uniprotID", "IndelSequenceAnchorSeq", "IndepPositioninGenome","Chrom","PacBio","region","PacBioStart","PacbioEnd","dot","strand","dot2","PacbioTranscriptID","ReferenceChrom","Reference_exon_start","Reference_exon_end", "dot3", "geneName", "strand2", "exontype","geneID","exonID","transcriptID","unkonwn")
}
#print(alignment.indel.detailed.info.table)
alignment.indel.detailed.info.table <<- alignment.indel.detailed.info.table
#print(alignment.indel.detailed.info.table)
}
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